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Next-generation sequencing

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https://www.readbyqxmd.com/read/29786923/biodiversity-of-the-human-oral-mycobiome-in-health-and-disease
#1
H M H N Bandara, C P Panduwawala, L P Samaranayake
The organisms that colonize the human body over a lifetime are diverse, extensive and gargantuan. A fair proportion of the microbiota that constitutes this human microbiome live within our oral cavities mostly as harmonious associates causing only sporadic disease. An important core constituent of the microbiome is the mycobiome, representing various fungal genera. Up until recently, only a few species of fungi, mainly Candida species, were thought to constitute the human oral mycobiome. The reasons for this are manifold, although the uncultivable nature of many fungi in conventional laboratory media, and their complex genetic composition seem to be the major factors which eluded their detection over the years...
May 22, 2018: Oral Diseases
https://www.readbyqxmd.com/read/29786897/targeted-next-generation-sequencing-for-the-diagnosis-of-patients-with-rare-congenital-anemias
#2
Noa Shefer Averbuch, Orna Steinberg-Shemer, Orly Dgany, Tanya Krasnov, Sharon Noy-Lotan, Joanne Yacobovich, Amir A Kuperman, Antonis Kattamis, Ayelet Ben Barak, Batia Roth-Jelinek, Evgeni Chubar, Evelyn Shabad, Gustavo Dufort, Martin Ellis, Ofir Wolach, Idit Pazgal, Abed Abu Quider, Hagit Miskin, Hannah Tamary
BACKGROUND: Most patients with anemia are diagnosed through clinical phenotype and basic laboratory testing. Nonetheless, in cases of rare congenital anemias, some patients remain undiagnosed despite undergoing an exhaustive workup. Genetic testing is complicated by the large number of genes involved in rare anemias and the similarities in the clinical presentation of the different syndromes. OBJECTIVE: We aimed to enhance the diagnosis of patients with congenital anemias by using targeted next-generation sequencing...
May 22, 2018: European Journal of Haematology
https://www.readbyqxmd.com/read/29786880/metagenomic-study-of-bacterial-microbiota-in-persistent-endodontic-infections-using-next-generation-sequencing
#3
G Sánchez-Sanhueza, H Bello-Toledo, G González-Rocha, A T Gonçalves, V Valenzuela, C Gallardo-Escárate
AIM: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS). METHODOLOGY: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified...
May 22, 2018: International Endodontic Journal
https://www.readbyqxmd.com/read/29786861/temporally-feathered-intensity-modulated-radiation-therapy-a-planning-technique-to-reduce-normal-tissue-toxicity
#4
Juan Carlos López Alfonso, Shireen Parsai, Nikhil Joshi, Andrew Godley, Chirag Shah, Shlomo A Koyfman, Jimmy J Caudell, Clifton D Fuller, Heiko Enderling, Jacob G Scott
PURPOSE: Intensity modulated radiation therapy (IMRT) has allowed optimization of three-dimensional spatial radiation dose distributions permitting target coverage while reducing normal tissue toxicity. However, radiation-induced normal tissue toxicity is a major contributor to patients' quality of life and often a dose-limiting factor in the definitive treatment of cancer with radiation therapy. We propose the next logical step in the evolution of IMRT using canonical radiobiological principles, optimizing the temporal dimension through which radiation therapy is delivered to further reduce radiation-induced toxicity by increased time for normal tissue recovery...
May 22, 2018: Medical Physics
https://www.readbyqxmd.com/read/29785653/valproic-acid-treatment-response-in-vitro-is-determined-by-tp53-status-in-medulloblastoma
#5
Bruna Mascaro-Cordeiro, Indhira Dias Oliveira, Francine Tesser-Gamba, Lorena Favaro Pavon, Nasjla Saba-Silva, Sergio Cavalheiro, Patrícia Dastoli, Silvia Regina Caminada Toledo
PURPOSE: Histone deacetylate inhibitors (HDACi), as valproic acid (VA), have been reported to enhance efficacy and to prevent drug resistance in some tumors, including medulloblastoma (MB). In the present study, we investigated VA role, combined to cisplatin (CDDP) in cell viability and gene expression of MB cell lines. METHODS: Dose-response curve determined IC50 values for each treatment: (1) VA single, (2) CDDP single, and (3) VA and CDDP combined. Cytotoxicity and flow cytometry evaluated cell viability after exposure to treatments...
May 22, 2018: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/29785639/development-of-a-molecular-diagnostic-test-for-retinitis-pigmentosa-in-the-japanese-population
#6
Akiko Maeda, Akiko Yoshida, Kanako Kawai, Yuki Arai, Ryutaro Akiba, Akira Inaba, Seiji Takagi, Ryoji Fujiki, Yasuhiko Hirami, Yasuo Kurimoto, Osamu Ohara, Masayo Takahashi
PURPOSE: Retinitis Pigmentosa (RP) is the most common form of inherited retinal dystrophy caused by different genetic variants. More than 60 causative genes have been identified to date. The establishment of cost-effective molecular diagnostic tests with high sensitivity and specificity can be beneficial for patients and clinicians. Here, we developed a clinical diagnostic test for RP in the Japanese population. STUDY DESIGN: Evaluation of diagnostic technology, Prospective, Clinical and experimental study...
May 21, 2018: Japanese Journal of Ophthalmology
https://www.readbyqxmd.com/read/29785615/molecular-characterization-of-proton-beam-induced-mutations-in-soybean-using-genotyping-by-sequencing
#7
Woon Ji Kim, Jaihyunk Ryu, Juhyun Im, Sang Hun Kim, Si-Yong Kang, Jeong-Hee Lee, Sung-Hwan Jo, Bo-Keun Ha
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS)...
May 21, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29785541/new-observations-in-tumor-cell-plasticity-mutational-profiling-in-a-case-of-metastatic-melanoma-with-biphasic-sarcomatoid-transdifferentiation
#8
Niels J Rupp, Markus Rechsteiner, Sandra N Freiberger, Daniela Lenggenhager, Mirjana Urosevic, Irene A Burger, Elisabeth J Rushing, Daniela Mihic-Probst
We describe a highly unusual case of metastatic melanoma in a 61-year-old female that manifested as a single groin lymph node metastasis accompanied by two distinct, subcutaneous sarcomatoid tumors on the same leg, without evidence of a primary tumor. Characterization encompassed extensive immunohistochemical staining as well as next-generation sequencing (NGS). The lymph node metastasis showed obvious features of melanoma. The two subcutaneous lesions, however, were morphologically and immunohistochemically consistent with high-grade myxofibrosarcoma and soft tissue mixed tumor, respectively...
May 21, 2018: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#9
Umay Kulsum, Arti Kapil, Harpreet Singh, Punit Kaur
Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29785397/whole-genome-sequencing-of-greater-amberjack-seriola-dumerili-for-snp-identification-on-aligned-scaffolds-and-genome-structural-variation-analysis-using-parallel-resequencing
#10
Kazuo Araki, Jun-Ya Aokic, Junya Kawase, Kazuhisa Hamada, Akiyuki Ozaki, Hiroshi Fujimoto, Ikki Yamamoto, Hironori Usuki
Greater amberjack ( Seriola dumerili ) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29785153/prevalence-of-deleterious-mutations-among-patients-with-breast-cancer-referred-for-multigene-panel-testing-in-a-romanian-population
#11
Iulian Gabriel Goidescu, Gabriela Caracostea, Dan Tudor Eniu, Florin Vasile Stamatian
Aim: Multigene panel testing for Hereditary Breast and Ovarian Cancer (HBOC) using next generation sequencing is becoming more common in medical care.We report our experience regarding deleterious mutations of high and moderate-risk breast cancer genes (BRCA1/2, TP53, STK11, CDH1, PTEN, PALB2, CHEK2, ATM), as well as more recently identified cancer genes, many of which have increased risk but less well-defined penetrance. Methods: Genetic testing was performed in 130 consecutive cases with breast cancer referred to our clinic for surgical evaluation and who met the 2016 National Comprehensive Cancer Network (NCCN) criteria for genetic testing...
2018: Clujul Medical (1957)
https://www.readbyqxmd.com/read/29785135/mutation-analysis-of-brca1-2-mutations-with-special-reference-to-polymorphic-snps-in-indian-breast-cancer-patients
#12
Nidhi D Shah, Parth S Shah, Yash Y Panchal, Kalpesh H Katudia, Nikunj B Khatri, Hari Shankar P Ray, Upti R Bhatiya, Sandip C Shah, Bhavini S Shah, Mandava V Rao
Background: Germline mutations BRCA1 and BRCA2 contribute almost equally in the causation of breast cancer (BC). The type of mutations in the Indian population that cause this condition is largely unknown. Purpose: In this cohort, 79 randomized BC patients were screened for various types of BRCA1 and BRCA2 mutations including frameshift, nonsense, missense, in-frame and splice site types. Materials and methods: The purified extracted DNA of each referral patient was subjected to Sanger gene sequencing using Codon Code Analyzer and Mutation Surveyor and next-generation sequencing (NGS) methods with Ion torrent software, after appropriate care...
2018: Application of Clinical Genetics
https://www.readbyqxmd.com/read/29785087/transcriptomic-impacts-of-rumen-epithelium-induced-by-butyrate-infusion-in-dairy-cattle-in-dry-period
#13
Ransom L Baldwin, Robert W Li, Yankai Jia, Cong-Jun Li
The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function...
2018: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/29785078/detection-of-hyper-conserved-regions-in-hepatitis-b-virus-x-gene-potentially-useful-for-gene-therapy
#14
Carolina González, David Tabernero, Maria Francesca Cortese, Josep Gregori, Rosario Casillas, Mar Riveiro-Barciela, Cristina Godoy, Sara Sopena, Ariadna Rando, Marçal Yll, Rosa Lopez-Martinez, Josep Quer, Rafael Esteban, Maria Buti, Francisco Rodríguez-Frías
AIM: To detect hyper-conserved regions in the hepatitis B virus (HBV) X gene ( HBX ) 5' region that could be candidates for gene therapy. METHODS: The study included 27 chronic hepatitis B treatment-naive patients in various clinical stages (from chronic infection to cirrhosis and hepatocellular carcinoma, both HBeAg-negative and HBeAg-positive), and infected with HBV genotypes A-F and H. In a serum sample from each patient with viremia > 3.5 log IU/mL, the HBX 5' end region [nucleotide (nt) 1255-1611] was PCR-amplified and submitted to next-generation sequencing (NGS)...
May 21, 2018: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29785006/the-era-of-immunogenomics-immunopharmacogenomics
#15
REVIEW
Makda Zewde, Kazuma Kiyotani, Jae-Hyun Park, Hua Fang, Kai Lee Yap, Poh Yin Yew, Houda Alachkar, Taigo Kato, Tu H Mai, Yuji Ikeda, Tatsuo Matsuda, Xiao Liu, Lili Ren, Boya Deng, Makiko Harada, Yusuke Nakamura
Although germline alterations and somatic mutations in disease cells have been extensively analyzed, molecular changes in immune cells associated with disease conditions have not been characterized in depth. It is clear that our immune system has a critical role in various biological and pathological conditions, such as infectious diseases, autoimmune diseases, drug-induced skin and liver toxicity, food allergy, and rejection of transplanted organs. The recent development of cancer immunotherapies, particularly drugs modulating the immune checkpoint molecules, has clearly demonstrated the importance of host immune cells in cancer treatments...
May 21, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29785005/nanopore-sequencing-technology-a-new-route-for-the-fast-detection-of-unauthorized-gmo
#16
Marie-Alice Fraiture, Assia Saltykova, Stefan Hoffman, Raf Winand, Dieter Deforce, Kevin Vanneste, Sigrid C J De Keersmaecker, Nancy H C Roosens
In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region. This DNA walking is performed on transgenic elements, commonly found in GMO, that were earlier detected by real-time PCR (qPCR) screening. Previously, we have demonstrated the ability of this approach to detect unauthorized GMO via the identification of unique transgene flanking regions and the unnatural associations of elements from the transgenic cassette...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29783834/-application-of-next-generation-sequencing-in-clinical-microbial-research
#17
L Y Guo, Q J Li, G Liu
No abstract text is available yet for this article.
May 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29783823/-phenotypic-and-genotypic-spectra-of-patients-with-glucose-6-phosphate-dehydrogenase-deficiency-gene-known-pathogenic-variants-a-single-center-study
#18
X Chen, L Yang, H J Wang, B B Wu, Y L Lu, X R Dong, W H Zhou
Objective: To analyze the hotspots of known pathogenic disease-causing variants of glucose-6-phosphate dehydrogenase (G6PD) and the phenotype spectrum of neonatal patients with known pathogenic disease-causing variants of G6PD. Methods: The known pathogenic disease-causing variants of G6PD were collected from Human Gene Mutation Database. Screening was performed for these variants among the 7 966 cases (2 357 neonatal, 5 609 non-neonatal) in the database of sequencing at Molecular Diagnosis Center, Children's Hospital of Fudan University...
May 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29783665/identification-of-novel-somatic-tp53-mutations-in-patients-with-high-grade-serous-ovarian-cancer-hgsoc-using-next-generation-sequencing-ngs
#19
Marica Garziera, Erika Cecchin, Vincenzo Canzonieri, Roberto Sorio, Giorgio Giorda, Simona Scalone, Elena De Mattia, Rossana Roncato, Sara Gagno, Elena Poletto, Loredana Romanato, Franca Sartor, Jerry Polesel, Giuseppe Toffoli
Somatic mutations in TP53 are a hallmark of high-grade serous ovarian cancer (HGSOC), although their prognostic and predictive value as markers is not well defined. Next-generation sequencing (NGS) can identify novel mutations with high sensitivity, that may be repurposed as potential druggable anti-cancer targets and aid in therapeutic decisions. Here, a commercial NGS cancer panel comprising 26 genes, including TP53 , was used to identify new genetic markers of platinum resistance and patient prognosis in a retrospective set of patients diagnosed with epithelial ovarian cancer...
May 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29782024/investigation-of-rna-synthesis-using-5-bromouridine-labelling-and-immunoprecipitation
#20
Rikke H Kofoed, Cristine Betzer, Søren Lykke-Andersen, Ewa Molska, Poul H Jensen
When steady state RNA levels are compared between two conditions, it is not possible to distinguish whether changes are caused by alterations in production or degradation of RNA. This protocol describes a method for measurement of RNA production, using 5-Bromouridine labelling of RNA followed by immunoprecipitation, which enables investigation of RNA synthesized within a short timeframe (e.g., 1 h). The advantage of 5-Bromouridine-labelling and immunoprecipitation over the use of toxic transcriptional inhibitors, such as α-amanitin and actinomycin D, is that there are no or very low effects on cell viability during short-term use...
May 3, 2018: Journal of Visualized Experiments: JoVE
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